How do I fix a scene with zero users?
Edit 2: the bug has been fixed on Blender side - so if you try the latest 2.83 beta build, you shouldn't have this issue anymore.

Having the same issue and from my tests it seems related to the new undo system introduced in 2.83 beta. Scenes can (randomly?) see their user count drop to 0 after an undo operation. Saving and re-opening the file temporarily fix that, but next undo may have the same effect.
It can become harmful if you use the "Purge All" action to clean orphan data, because those 0-user scenes will be considered as such and therefore deleted.

Edit: I've reported this issue here.

It does not happen (at least in my tests) when using "Undo Legacy".


Preferences > Interface > Developer Extras
Preferences > Experimental > Undo Legacy